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ABSTRACT
RNA secondary structures can be divided into helical regions composed of canonical WatsonCrick and related basepairs, as well as single-stranded regions such as hairpin loops, internal
loops, and junctions. These elements function as building blocks in the design of diverse RNA
molecules with various fundamental functions in the cell. To better understand the intricate
architecture of three-dimensional RNAs, we analyze existing RNA 4-way junctions in terms of
basepair interactions and three-dimensional configurations. Specifically, we identify nine broad
junction families according to coaxial stacking patterns and helical configurations. We find that
helices within junctions tend to arrange in roughly parallel and perpendicular patterns, and
stabilize their conformations using common tertiary motifs like coaxial stacking, loop-helix
interaction, and helix packing interaction. Our analysis also reveals a number of highly
conserved basepair interaction patterns and novel tertiary motifs such as A-minor-coaxial
stacking combinations and sarcin/ricin motif variants. Such analyses of RNA building blocks can
ultimately help in the difficult task of RNA 3D structure prediction.
Keywords: RNA structure; 4-way junction; tertiary motifs; coaxial stacking; non-Watson-Crickbasepair
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INTRODUCTION
Recent studies have demonstrated the amazing capacity of RNA to form complex tertiary
structures as well as perform many surprisingly intricate cellular functions1; 2; 3. As new roles for
RNAs are being discovered, the functionality of many non-coding RNAs remains unknown4.
RNA crystallography has offered unprecedented opportunities to analyze RNA tertiary (3D)
structure5;
6; 7; 8; 9
and relate structure to function. RNA molecules have also been studied
extensively at the secondary-structure level, where building blocks include helical stems and
single-stranded regions such as hairpins, bulges, internal loops, and junctions. In particular a
junction – defined as the point of connection between different helical segments10– is a common
structural element found in a wide range of contexts from within small RNA structures11; 12 to the
large ribosomal subunits9; 13; 14. These structural elements have well defined 3D configurations
that are important in the organization of the global structure of RNA molecules. While more is
known about hairpins and internal loops15, our current understanding of the more complex
junction elements is limited. An advance in our knowledge of junctions is important because
junctions define main architectural building blocks of RNA tertiary arrangements. In particular,
to better understand how RNAs function, a quantitative analysis of these important structural
elements is needed.
Experimental techniques such as NMR and crystallography have produced a number of high
resolution RNA 3D structures16, allowing researchers to observe and study some structural
properties of junctions such as coaxial stacking of helices and long-range tertiary interactions12;
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4
. For instance, Lilley et al.20; 21; 22 analyzed the conformations of specific examples of 3-
way and 4-way junctions (junctions composed of three and four helical arms, respectively) in
nucleic acids using FRET techniques, and observed transitional changes in their helical
configuration under Mg2+ and Na+ concentration variations. Lescoute and Westhof23 compiled
and analyzed the topology of three-way junctions in folded RNAs, specifying rules to predict
coaxial stacking, which occurs when two separate helical regions stack to form coaxial helices as
a pseudo-continuous helix (see Fig. 1b). Tyagi and Mathews24 also predicted coaxial stacking
based on free energy minimization and concluded that non-canonical basepairs make coaxial
stacking more difficult to predict. RNAJunction, a database developed by Bindewald et al.25,
contains information on RNA structural elements including junctions.
Our previous work on annotation and analysis of RNA tertiary motifs19, based on a
representative set of high-resolution RNA structures, showed that coaxial helices are abundant
tertiary motifs that often cooperate with other long-range interactions such as A-minor to
stabilize RNA’s structure. Motivated by these results, we investigate here the structure of 4-way
junctions in more detail, using the currently available solved crystal structures of folded RNAs.
Our long-term goal is to find sequence “signatures” and other properties that will ultimately aid
the prediction of coaxial stacking patterns and helical configurations of a given RNA based
solely on sequence or computationally-predicted secondary structure. Our classification of nine
families of 4-way junctions here shows that helices within junctions arrange in roughly parallel
or perpendicular patterns, and stabilize their conformations using common tertiary motifs.
Within junctions we also encounter novel tertiary motifs such as A-minor-coaxial stacking
combinations and sarcin/ricin motif variants.
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RESULTS
We begin with a classification of 4-way junctions based on their coaxial stacking, parallel and
perpendicular helix arrangement patterns, and configuration of their flexible helical arms. By
using the Leontis and Westhof notation26; 27, we study the associated basepair interactions and
describe common motifs. A helix here is required to contain at least two consecutive WatsonCrick (WC) basepairs (G-C, A-U and G-U). For convenience, we label and color code helices
sequentially according to the 5′ to 3′ orientation of the entire RNA as shown in Fig. 1. The single
stranded region between each pair of consecutive helices Hi and Hi+1 is labeled by Ji/i+1. The
point where strands exchange is called the point of strand exchange or simply crossover. A
relative rotation of one helical pair could be right handed (clockwise) or left handed
(counterclockwise)22.
Our list of 62 4-way junctions (Table 1) was assembled by taking all high-resolution RNA
structures from the Protein Data Bank16 as of April 2009. RNA 4-way junctions are the second
most abundant junction type after 3-way junctions. Previously Lescoute and Westhof23 analyzed
and divided RNA three-way junctions into three families according to their topology. As the
degree of helix branching increases, the number of possible junction conformers grows rapidly,
and the junctions become highly diverse in terms of possible interactions and motifs. This
diversity complicates classification of RNA junctions. However, a natural way to group them is
according to their coaxial stacking patterns and helical organization. Our list of 62 four-way
junctions (Table 1) is divided into nine families as shown on Fig. 2 (one diagram per RNA type).
Families H, cH and cL contain junctions with two coaxial stacking; families cK and  are formed
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by junctions with one coaxial stacking; and junctions in families cW, , X, and cX contain no
coaxial stacking (see name selections below). Our classification differs from that of Lilley on
DNA four-way junctions conformers22 in the sense that we group related conformers into one
family; however, we also distinguish between parallel and antiparallel conformers. See also
comment in Discussion on the flexibility and dynamic nature of RNA junctions. We now
describe each family in turn. The Leontis-Westhof notation is used in our annotation – see also
inset tables at the end of Fig. 2.
Four-way junction families
4-way junctions with two coaxial stacking
Family H is characterized by two coaxial stacking roughly aligned, resembling the letter H (see
Fig. 2a). The continuous strands in each coaxial helix are antiparallel to each other, resembling
the DNA Holliday junction4. The coaxial helices are stabilized by their long-range interactions
and, in some instances, these interactions contribute to small (left or right-handed) rotations (e.g.
hairpin ribozyme and ribonuclease P A-type in Fig. 2a) similar to the X-stacked conformer in
DNA 4-way junctions28.
Family cH also consists of two coaxial helices roughly aligned, but now the continuous strands at
each coaxial helix runs in the same direction (Fig. 2b). When viewed from a direction
perpendicular to the coaxial helix axis, the exchanging strands appear to cross at the center. Aminor interactions29 (denoted in Fig. 2 by empty and solid triangles known as Sugar-Sugar
interactions) are the most conserved interactions responsible of such crossings at the point of
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strand exchange, as we discuss below in more detail. Note that two types of pairwise coaxial
stacking patterns are observed: H1H4 with H2H3, and H1H2 with H3H4.
In family cL, the pair of coaxial stacks H1H4 and H2H3 aligns in a perpendicular fashion, making
an “L” shape. The most well known structure in this family is the transfer RNA12. The “L” shape
can be stabilized by a diversity of long-range interactions such as loop-loop, loop-helix, or helix
packing interactions such as P-interactions30;
31
(Fig. 2c), but other factors such as ion
concentrations also play a role. As in family H, A-minor interactions within the junction domain
anchor single stranded regions to the end of its helices to produce crossing at the point of strand
exchange. Note that the riboswitch (2GIS_7) represents a different conformer from the three
examples in Fig. 2c, because the coaxial helix H2H3 is rotated relative to H1H4 so that helices H1
and H3 are sufficiently close to interact.
4-way junctions with one coaxial stack
Family cK consists of two helical arms stacked, while the third helix becomes perpendicular to
the coaxial helix, and the fourth subtends an angle that depends on the number of unpaired bases
and tertiary interactions (Fig. 2d). Long-range interactions help stabilize the perpendicular
helical arrangement. Family cK also contains a crossing at the point of strand exchange, usually
formed by adenine bases that make up A-minor interactions at the locus of the strand exchange.
In addition, helix packing interactions, pseudoknots, and other types of non-canonical basepair
interactions can help rotate the helical arm and produce the same perpendicular arrangement.
Three types of junction conformers can be noted, each with one coaxial stacking (H1H2, H3H4,
and H1H4), and one helix perpendicular to them (H4, H2 and H3 respectively).
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Note that in the 16S rRNA 2AVY_114 (Fig. 2d), both H2 and H3 are perpendicular to each other
and to the coaxial helix, forming a perpendicular frame in three-dimensional space.
Family  resembles family H but instead of the two coaxial stacking interactions of family H,
family  has only one, with the second pair of helices aligned rather than stacked. The
ribonuclease P structure (1U9S_118) uses non-canonical basepair interactions32 to reduce the
instability caused by the long strands J1/2 and J2/3. Helix H2 is anchored to H3 through A-minor
interactions (Fig. 2e).
4-way junctions with no stacking
Families cW, , cX and X are less common and so far only observed within the large ribosomal
structures 16S and 23S rRNA. They are characterized by longer single-strand elements and no
coaxial stacking, but they contain at least one helical alignment or perpendicular helix
interaction. Like the other families, they also contain a high degree of junction symmetry. The
specific conformations depend on the tertiary interactions that form, as well as the binding of
proteins. Family cW has a helical alignment between consecutive helical arms H1 and H4 (Fig.
2f). Family  has also a helical alignment, but is defined by the two non-consecutive helical
arms H2 and H4 (Fig. 2g). Families cX and X contain 4-way junctions with helical arms in
perpendicular arrangements (Fig. 2h-i). The junction in family X has a non-planar triad of helices
roughly perpendicular to each other, while family cX has two pairs of helical arms arranged
perpendicular to each other by helix packing interactions.
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Tertiary motifs in four-way junctions
Our analysis underscores the diversity of RNA 4-way junction in structure. Still, common
features such as sequence and stacking preferences, loop sizes, basepair interactions, and tertiary
motifs are often preserved within and across families, as we describe next.
Coaxial stacking
Coaxial stacking is a common tertiary motif present in many junctions, as well as internal loops,
and even pseudoknots and kissing hairpins18; 19. From our list of 62 4-way junctions (Table 1),
which contains 75 cases of coaxial stacking, about 33 (53%) of the junctions contain two coaxial
stacking interactions (Fig. 2a-c), 14 (22%) contain one coaxial stacking (Fig. 2d-e), and the
remaining 17 (27%) of the junctions contain no coaxial stacking (Fig. 2f-i).
Table 2 describes the frequency of these 75 coaxial stacking cases in our dataset of 62 4-way
junctions (Table 1), ordered by size of loop Ji/i+1 between the helices Hi and Hi+1 forming the
stacking. A strong preference for stacking between helices with small loop size Ji/i+1 (between 0
and 1) can be observed. Similar patterns have been reported for 3-way junctions23. As the size of
Ji/i+1 increases, coaxial stacking between helices becomes less likely and no coaxial stacking with
Ji/i+1>7 was observed. Note that a small loop size does not guarantee coaxial stacking (see for
instance the lengths of J1/2 and J3/4 for junctions on family H in Fig. 2a).
Interestingly, from the list of observed coaxial helices in our dataset of junctions (Table 1), we
note a strong preference for stacking between H1H4 and H2H3. A total of 30 (40%) and 28 (38%)
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out of 74 coaxial helices are formed between H1H4 and H2H3, respectively (the hairpin ribozyme
1M5O_13 was excluded here since this junction is formed by two strands, making it difficult to
label the first helix). Furthermore, 28 (93%) out of the 30 four-way junctions with two coaxial
stacking form both H1H4 and H2H3 patterns. Although the reason for these strong coaxial
stacking preferences is unclear, we speculate that this is related to the right-handedness of RNA
molecules.
Coaxial stacking interactions also occur in helical stems that form pseudoknots33. In fact,
pseudoknots involving single stranded loops regions Ji/i+1 in junctions will facilitate coaxial
stacking between helices Hi and Hi+1 as observed in 16S rRNA 2AVY_18 and 23S rRNA
1S72_1452 in Fig. 2d.
Non-canonical basepairs are frequently formed between loops Ji-1/i and Ji/i+1 next to their common
helix Hi. These non-canonical basepairs stack to Hi to reduce the number unpaired nucleotides
between Ji-1/i or Ji/i+1 and help promote coaxial stacking between Hi and a neighboring helix. It has
been previously reported that sheared GA basepairs (trans Hoogsteen/Sugar) of cis WC GA
occur often at the end of helices34; 35. Other basepairs such as the AU trans Hoogsteen/Watson
are also frequent like observed in Fig. 2. In agreement with previous studies on three-way
junctions36, the stability of junctions depends on the amount of unpaired nucleotides at the Ji/i+1
regions. Thus, not only is the length of Ji/i+1 important in coaxial stacking, but the non-canonical
basepair formation plays also an important role as well.
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Parallel and perpendicular helical configurations
A small number of helical arms align their axis without stacking forces, or arrange in roughly
perpendicular configurations (Fig. 2f-i). This is not exclusive of junctions18. Parallel
conformations between helices are stabilized using long-range interactions, preferably A-minor
interactions as in the case of 23S rRNA 2AW4_1443 in Fig. 2b, but other basepairs such as WC
GC basepairs and even base-backbone interactions are frequent. The dotted-line interactions in
Fig. 2 denote one hydrogen bond or base-backbone interactions that do not fit into the base-base
classification of Leontis and Westhof. Helices that arrange in perpendicular configurations are
often stabilized by helix packing interactions such as the P-interaction30; 31 between WC GU
wobble basepairs on a first helix and a WC basepair in a second helix (see for instance 23S
rRNA 2AW4_600 in Fig. 2i). This P-interaction functions by anchoring the former helix into the
minor groove of the latter. Loop-helix and loop-loop interactions that stabilize perpendicular
helix configurations also occur, as in the case of the 23S rRNA 2J01_1269 in Fig. 2c and the
tRNA D-loop/T-loop interaction37 (see tRNA 1EHZ_6 in Fig. 2c). Besides P-interactions, other
forms of interactions are of course possible, requiring a larger dataset of junctions.
A-minor and other sugar-edge interactions
A-minor motifs are among the most abundant tertiary interactions found in RNA. In our recent
annotation of a representative high-resolution set of solved RNA, A-minor interactions were
observed in 37% of the tertiary motifs. A-minor motifs involve sugar-edge interactions which
can be recognized in the diagrams by the small connector triangles between adenines located in
single stranded regions, and the helical receptor, usually a WC (GC) basepair. We previously
reported that the helical receptor of A-minor has a strong preference to lie at the end of helices
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rather the inside helices19. Our data here indicate that A-minor interactions within junctions form
two main types of motifs.
The first and most common interaction often involves two adenines (but it could also be one or
three adenines) in the loop region Ji/i+1 forming sugar-edge interactions, often A-minor (type I
and II), but also cis Sugar-Hoogsteen and cis Watson-Sugar (e.g. HCV IRES domain 1KH6_4 in
Fig. 2a). These adenines interact with helical elements of the junction near the end of the helix
(see Fig. 3a), forming a crossing at the point of strand exchange. Several examples are found in
junction families cH, cL and cK.
As was previously observed in 3-way junctions23, the right handedness of RNA implies that
when a coaxial stacking between helices say Hi and Hi+1 is formed, the 5′-end strand entering Hi
faces the shallow/minor groove of Hi+1, thus allowing nucleotides in Ji-1/i to interact with Hi+1 as
sugar-edge interactions (see Fig. 3a). This property reflects the occurrence of the A-minor (and
other sugar-edge) interactions described above. By analyzing cases of A-minor/coaxial stacking
interactions across several families, we constructed a consensus diagram in Fig. 3b. Here N
denotes a small number of nucleotides (0 to 3); the same number is required on both loop
strands. X-X denotes standard WC basepairs (GC, AU) and the GU wobble basepair. If a
pseudoknot forms between helices which appear stacked, the adenines can also interact with the
helix produced by this pseudoknot (see for instance 23S rRNA 1S72_1452 in Fig. 2d). Because
this pattern occurs very often, we consider it an important functional arrangement of helices.
Similar interactions between pseudoknots and A-minor motif has been previously observed19.
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A second and less common interaction involving A-minor occurs when either the 5′-end or the
3′-end strand leaving the helix makes a u-turn and interacts again with its starting helix (Fig. 3c).
A number of nucleotides M are needed (2 to 3) to allow the u-turn. A case is observed on 16S
rRNA 2J00_568 in Fig. 2c when two nucleotides in M form a pseudoknot with another RNA
strand, thus reorienting the 5′-end strand back to its starting helix. A second example is found on
and 23S rRNA 2J01_1832 in Fig. 2g where adenines in J4/1 interacts with helix H1.
One interesting example exists in the 23S rRNA (see Fig. 2g, 2J01_1832 in family ) where the
direction of the A-minor interaction pattern is reversed. A pair of adenines in J3/4 interacts with
helix H2 rather than H1. This interaction can be explained by the fact that RNA is for the most
part a right handed molecule, but in this junction, due to the sarcin/ricin like motif inside, a
portion of the loop strand J3/4 folds in a left-handed orientation, thus reversing the direction of the
pattern shown in Fig. 3a. Sarcin/ricin like motifs are described in more detail next.
Sarcin/ricin like motifs
A different type of tertiary interaction resembling the sarcin/ricin motif32 occurs within the
single-stranded regions of junctions, particularly for members of families  and cX. Sarcin/ricin
like interactions appear on junctions where helical alignment rather than coaxial stacking is
present. These interactions show a surprising similarity to the sarcin/ricin motif. However, they
lack the AG (shown in Fig. 4 in green) trans Hoogsteen-Sugar or the AA trans HoogsteenHoogsteen (orange in Fig. 4), as well as all UC trans Sugar-Hoogsteen basepair interactions
(cyan in Fig. 4). As in sarcin/ricin motifs38, these interactions stabilize RNA-RNA conformations
as shown in Fig. 4 (magenta), as well as RNA-protein interactions (red color in Fig. 4).
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DISCUSSION
Annotating and analyzing is a major task in structural biology. For RNA, classification and other
aspects of RNA structure and function have provided much work for many researchers under the
RNA Ontology Consortium (ROC)39 (http://roc.bgsu.edu/). The notion of classes as discussed
here for 4-way junctions is important for understanding common properties that members of a
family share. Ultimately, such classification can help interpret RNA function.
The classification of 4-way junctions considered here is a complementary and compatible
approach to the classification of RNA 3-way junctions given by Lescoute and Westhof23, which
groups elements according to their topology. RNA junctions listed in the RNAJunction25
database have been classified according to standard nomenclature10 based on the size of each
loop region. However, similar junctions from homologous RNAs can differ by single insertions
of deletions in the loop regions, leading to different classifications under the standard
nomenclature. Similarly, the SCOR40 database lists examples of coaxial helices as elements of
tertiary motifs. Our work extends these definitions/classifications to all known coaxial helices
encountered in four-way junctions as of October 2008. The previous classification of DNA 4–
way junctions22 is only based on forms containing two coaxial helices, whereas our framework
additionally includes junctions that contain one or no-coaxial stacking.
The classification presented here identifies nine major families of 4-way junctions; other
conformations and families are of course theoretically possible. For each example in Fig. 2a, we
observed a stacking of helices H1H4, and H2H3, but the conformer H1H2 and H3H4 might exist in
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nature. Although not yet observed, one can also imagine the existence of family L where pairs of
coaxial stacking align in a perpendicular fashion but without the crossing of the single strands at
the point of strand exchange. Similarly, one can predict the existence of a family K where the
crossings at the point of strand exchange is not present. Conformations also include members in
family  yet to be discovered with a high degree of rotation between the inter-helical angles of
H1H2 with H3H4, instead of the almost parallel conformer of ribonuclease P 1U9S_118 as we
observed in Fig. 2e.
In general, due to the conformational flexibility and dynamic character of 4-way junctions, a
continuum of junction conformations might be possible. Still, current structural information
suggests a preference for conformations consisting of parallel and perpendicular helical
arrangements. Thus, new conformations will likely oscillate around these observed families and
possibly new ones such as the families L and K that we define. We are currently extending this
work to all higher order junctions available (Laing et al., in preparation41).
The data from Table 2 reveal a high frequency of coaxial stacking of helices when the size of
their common single stranded loop is small; we also note certain sequence preferences and that
the presence of pseudoknots can strongly induce coaxial stacking. Our analysis reveals a strong
tendency for coaxial stacking between helices H1 with H4 and H2 with H3. Although the reason
for this is unclear, we speculate that the right handedness of RNA has a role. Additionally, such
topologies could be favored during RNA transcription because helices that form first could have
a greater opportunity to stack first. Furthermore, in the large ribosomal RNA, proteins that bind
to sites in the junction near the 5′-end of the starting helix may assemble earlier than those
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located near the 3′-end; thus, those proteins buried in the interior of junctions influence the
coaxial stacking formation by enhancing or restricting conformational flexibility of the helical
arms.
One advantage of grouping junctions is that it allows recognizing important repeating motifs
such as the sugar-edge interactions (mostly A-minor interactions) and the sarcin/ricin like motifs.
These sets of non-canonical basepairs play important roles in RNA’s structure and therefore
function. For instance, it has been reported42 that mutations on the adenines in the loop regions of
the 4-way junction (HCV IRES domain 1KH6_4 in Fig. 2b) in the HCV IRES RNA are lethal to
the virus; thus, the sugar-edge interactions are critical elements for the correct structure of the
junction. Another example showing the importance of these long-range interactions is found in
the hairpin ribozyme (1M5O_13 in Fig. 2a). While this ribozyme can be active in the absence of
the junction, under physiological ionic conditions the junction’s presence accelerates the ioninduced folding of the ribozyme by 500-fold43. Sarcin/ricin like motifs are important structural
elements that stabilize the junctions when no coaxial stacking is present, but also serve as sites
for specific RNA-RNA and RNA-protein recognition. The existence of such variants of the
original sarcin/ricin motifs agrees with the idea of RNA modularity44 and the principle of
structural scaffolding45, where RNA motifs are stable interactions formed by submotifs. While
these submotifs are more versatile, they retain key structural tertiary interactions.
The junctions we encountered containing two coaxially-stacked elements belonging to families
H, cL and cH differ in the angle between the axes of the coaxial-stacks, roughly 0º, 90º or 180º
respectively. While the degree of rotation depends on the environment (e.g., ion concentration,
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proteins), the length of the loops forming the exchanging strands for each family also determines
its final conformation. For instance, the lengths of the loops in family H are small compared to
those found in the other families. In family cL, the lengths of the loops at the exchanging strands
are often larger than those in family H to allow the perpendicular rotation, while avoiding steric
clashes. In family cH, the lengths of the loops are slightly larger than in family H but smaller
than in cL; however, as previously mentioned, the presence of sugar-edge interactions help
stabilize the conformation (see Table S1).
Furthermore, A-minor or other sugar-edge interactions within junction domains are important
structural elements for excluding interconversion between families such as cH and H to one
another20. Correctly predicting A-minor interactions can help predict coaxial stacking patterns
since loops that contain adenines involved in A-minor interactions will not form coaxial stacking
with their neighboring helices. However, it is not clear whether these interactions will occur even
in the presence of consecutive adenines in loop regions. Such adenines could form stacking
interactions or long-range A-minor interactions with other RNA elements, or could interact with
proteins.
Indeed, experiments for the hammerhead ribozyme46 and hairpin ribozyme47 have shown that
loop-loop interactions act as important elements in the function of these ribozymes, by
stabilizing the correct conformation of these junctions. While more data will strengthen these
assertions, it clear that long-range interactions are important complementary elements in the
junction domains.
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Our compilation of RNA junction domains illustrates nature’s strong preferences for the
arrangement of RNA helical elements in parallel and perpendicular patterns. The conformations
of some 4-way junction elements also greatly resemble helical configurations of three-way
junctions. For instance, in the classification of Lescoute and Westhof23, the conformation given
in family C is a subset of our family cH, where in both cases a coaxial stack aligns in parallel to a
third helical arm which is stabilized by A-minor interactions. Similarly, 3-way junction elements
belonging to the Family A resemble the conformation observed for 4-way junctions in our family
cK.
The junction 2J01_1832 in family  shown in Fig. 2g is also of interest. Here the loop region J3/4
interacts with H2 using A-minor interactions, while near H3, it is structured like a hairpin using
the standard U-turn motif, and closed by a trans WC GC basepair. This U-turn behaves like a
small extra helix or a like a cap. The resulting motifs align H3 parallel to both H2 and H4. This
pattern is the characteristic signature of the 3-way junction elements of family C. Understanding
such preferences for RNA’s helical conformations can greatly improve RNA 3D structure
prediction. However, more work on understanding such topologies is required. Ongoing efforts
will continue to analyze higher order junctions.
Our analysis underscores the notion20 that RNA junctions are composed of both rigid and flexible
elements. Tertiary motifs such as coaxial stacking, pseudoknots and RNA-RNA long-range
interactions are interactions responsible for maintaining the rigid parts of the junction, while
flexible elements appear on helical arms with longer loop regions and are more sensitive to
external forces such as proteins and ion concentration. This is consistent with the fact that loop
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regions involved in RNA-protein interactions are consistently longer in size48; 49 and appear on
the large ribosomal subunits. FRET experiments also show changes on inter-helical angles at
high or low magnesium concentrations, with coaxial stacking interactions unchanged50.
Interestingly, the crystal structure of the 4-way junction HCV IRES domain solved by Kieft et
al.42 (1KH6_4 in Fig. 2b) describes one conformation containing a pair of coaxial stacks parallel
to each other. While only one conformer can be incorporated in the crystal lattice, studies using
comparative gel electrophoresis and FRET analysis have shown that this junction exists in a
dynamic equilibrium between parallel and antiparallel structural conformations51. In contrast, the
junction 2AW4_1443 (Fig. 2b) contains A-minor interactions outside the junction domain which
helps stabilize the parallel junction configuration; however, no long-range interactions are
observed in the HCV IRES crystal structure. Similar studies on the junction obtained by
removing the neighboring internal loops20 of the hairpin ribozyme (1M5O_13 from Fig. 2a) in
the presence of Mg2+ have shown a continuous interconversion between parallel and antiparallel
forms. These findings underscore the polymorphic and dynamic character of junctions as needed
for biological function, including interactions with other molecules.
Finally, we propose in Fig. 5 what could be described as the anatomy of a 4-way junction. The
idea is to build upon secondary structure features that can help predict three-dimensional shape
of junctions. Coaxial stacking occurs between helical arms with a small number of intervening
single stranded nucleotides. Non-canonical basepairs, preferably GA (sheared) trans SugarHoogsteen, or a AU trans Watson-Hoogsteen (or GC WC basepairs) can help to reduce the
number of nucleotides between helices by base stacking interactions. Also, internal basepair
interactions between non-consecutive loop elements of the junctions help reduce the spatial
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distance between helical arms, with the most common interaction involving AU trans WatsonHoogsteen or WC GC basepairs. Helix packing interactions such as P-interactions involving GU
cis WC near the end of the helix help promote perpendicular arrangements between helices.
Long-range interactions, preferably A-minor motifs, stabilize helical elements and align them in
parallel; for these interactions to form, hairpin loops or internal loops must exist near the junction
domain. Other types of RNA-RNA or RNA-protein interactions can occur at the single stranded
regions, but this requires longer loop chains. Analysis of higher-order junctions and other RNA
tertiary motifs will further help put these ideas into a growing framework of RNA architecture
and ultimately function.
MATERIALS AND METHODS
Data of our 3D RNA junctions were collected from the RCSB Protein Data Bank16. Based on
available structures as of April 2009, 554 high-resolution structures were selected with
repetitions omitted by choosing the more recent structures. Junction elements were searched
within these and analyzed for basepair interactions (see below).
Dataset of RNA junctions
To perform our comprehensive search of 4-way-junctions in the set of RNA structures above, we
first considered the secondary structure associated with every 3D structure defined in terms of its
WC basepairs (G-C, A-U and G-U) and the single stranded regions. The search for canonical
WC and wobble basepairs was performed using the program FR3D52. Next we searched for sets
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of four distinct strands connecting in a cyclical way by at least two consecutive canonical WC
basepairs (Fig. 1). For simplicity, pseudoknots were automatically removed during the search,
but later re-inserted for statistical analysis. Visual inspection was also used to verify the
correctness of our procedure. In addition, we compared our search outcome to data available
from the RNAJunction database25, to ensure the verity of all junctions.
Our search of 20 crystal structures contained at least one 4-way junction each. The structures
include the two high resolution crystal structures of the 16S (PDB 2AVY, 2J00) and four 23S
rRNA (PDB 1NKW, 1S72, 2AW4, 2J01). Although the 3D shape of homologous rRNA
molecules is highly conserved among species, differences are informative because they help to
understand evolutionary changes that Nature allows while keeping their molecular function
intact. In total, our dataset thus contains 62 four-way junctions as listed in Table 1. Additional
detailed junction information such as PDB source, sequence, and residue numbers are available
in Table S1 from the Supplementary Material.
Basepair Interactions and Coaxial Stacking
Non-canonical basepairing with alternate hydrogen bonding patterns occur often in RNA. A
consensus between FR3D and RNAVIEW53 was considered to classify basepairs. Where
discrepancies occur, we employed visual programs such as Pymol (DeLano Scientific LLC) and
Swiss PDB viewer54 to clear the analysis. Additionally, the junction data were analyzed from
different perspectives: sequence signatures, length of loop regions, 3D motifs, and the 3D
organization of their helices. Orientation aspects such as in coaxial stacking, helices that form
Laing and Schlick
22
perpendicular inter-helical angles, and helices aligning their axis in parallel without the use of
stacking forces were analyzed on the basis of inspection.
Network Interaction Diagrams
Network interaction diagrams describing basepair interactions are represented symbolically
according to the Leontis and Westhof basepairing classification26; 27. The diagrams were created
using S2S55, a visual aid program based on RNAVIEW. We also used the 3D visual program
Pymol to classify 4-way junctions into families.
FUNDING
The work was supported by the Human Frontier Science Program (HFSP), by a joint
NSF/NIGMS initiative in Mathematical Biology (DMS-0201160), by NSF EMT award # CF0727001. Partial support by NIH (grant # R01-GM055164), NIH (grant # 1 R01 ES 012692), and
NSF (grant # CCF-0727001) is also gratefully acknowledged. The authors thank Abdul Iqbal and
Segun Jung for their help in figure preparation.
Laing and Schlick
23
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